Aim: To give an overview of the microbiology of blood and wound samples from surgical site infections (SSIs) after gastrointestinal surgery, as well as the antimicrobial susceptibility of the microorganisms involved, and to discuss the appropriateness of the prophylactic antibiotics administered. Materials & methods: During a 3.5-year study period, wound swabs and blood samples of patients with an SSI were taken in the first 48 h after surgery until 30 days thereafter. Results: Most pathogens were isolated from wound swabs. Escherichia coli (25%) and Pseudomonas aeruginosa (10%) were the most frequently found microorganisms. Both microorganisms showed a slight tendency towards a decrease in susceptibility for the tested antibiotics, although after correction, this was not significant. Conclusion: The comparison between wound swabs taken in the first 48 h after a surgical procedure and swabs in the 30 days thereafter provides important information concerning the microbiology of SSIs and the development of antibiotic resistance of the causative agents over time.